Objectives The action of stress hormones, mainly glucocorticoids, starts and coordinates the systemic response to stressful events. The HPA axis activity is predicated on information processing and modulation by upstream centres, such as the hippocampus where adult‐born neurons (hABN) have been reported to be an important component in the processing and integration of new information. Still, it remains unclear whether and how hABN regulates HPA axis activity and CORT production, particularly when considering sex differences. Materials and Methods Using both sexes of a transgenic rat model of cytogenesis ablation (GFAP‐Tk rat model), we examined the endocrinological and behavioural effects of disrupting the generation of new astrocytes and neurons within the hippocampal dentate gyrus (DG). Results Our results show that GFAP‐Tk male rats present a heightened acute stress response. In contrast, GFAP‐Tk female rats have increased corticosterone secretion at nadir, a heightened, yet delayed, response to an acute stress stimulus, accompanied by neuronal hypertrophy in the basal lateral amygdala and increased expression of the glucocorticoid receptors in the ventral DG. Conclusions Our results reveal that hABN regulation of the HPA axis response is sex‐differentiated. Cytogenesis ablation in the adult brain of female rats leads to HPA axis disruption. Female, but not male, GFAP‐Tk rats show increased corticosterone secretion at nadir, a heightened, yet delayed, response to an acute stress, neuronal hypertrophy in the basal lateral amygdala and increased glucocorticoid receptor expression in the ventral DG. These results reveal a sex‐differentiated hABN regulation of the HPA axis response.